annotate VCF files for poly repeats
meta
:map
Groovy Map containing VCF information
vcf
:file
Groovy Map containing reference genome information for vcf
*.{vcf,bcf,vcf.gz,bcf.gz}
tbi
Alternative VCF file index
*.tbi
regions_file
Regions file
meta2
Groovy Map containing fasta information
fasta
Groovy Map containing reference genome information for fai reference fasta file
*.fasta
meta3
Groovy Map containing fasta.fai information
fai
Groovy Map containing reference genome information for fai
*.fasta.fai
meta4
Groovy Map containing fasta.dict information
dict
Groovy Map containing reference genome information for GATK sequence dictionary
*.dict
Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]
*.${extension}
VCF filtered output file
csi
*.csi
Default VCF file index
versions
versions.yml
File containing software versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
